1. Transcriptional regulation
Chapter 18 Opener
Transcriptional regulation
Chapter 18 Opener
Transcriptional regulation

2. Principles of Transcriptional Regulation
Gene expression is controlled by regulatory proteins.
Most activators and repressors are act at the level of transcription initiation.
Many promoters are regulated by activators that help RNA polymerase bind DNA and by repressors that block that binding.

3. Principles of Transcriptional Regulation
Some activators and repressors works by allostery and regulate steps in transcriptional initiation after RNA polymerase binding.
Action at a distance and DNA looping
Cooperative binding and allostery have many roles in gene regulation.
Antitermination and beyond: Not all of gene regulation targets transcriptional initiation

4. Regulation of transcription initiation: examples from prokaryotes
An activator and a repressor together control the lac genes
CAP and Lac repressor have opposing effects on RNA polymerase
CAP has separate activating and DNA binding surfaces

5. Figure 18-1
Activation by recruitment of RNA polymerase by regulatory proteins (activator)
(constitutive expression: basal level – RNA pol occasionally bind)
Figure 18-1
Activation by recruitment of RNA polymerase
(constitutive expression: basal level – RNA pol occasionally bind) 5

6. Figure 18-2
Some activators and repressors works by allostery and regulate steps in transcriptional initiation after RNA polymerase binding.
RNA pol binds but no transcription
Figure 18-2
RNA pol binds but no transcription
works by allostery 6

7. Interactions between proteins bound to DNA
Figure 18-3
Interactions between proteins bound to DNA
Cooperative binding of proteins to adjacent sites
Action at a distance and DNA looping
Figure 18-3
Cooperative binding of proteins to adjacent sites 7

8. Figure 18-4
A DNA-bending protein can facilitate (가능하게 하다) interaction between distantly bound DNA binding proteins.
Figure 18-4 8

9. Regulation of transcription initiation : examples from prokaryotes
Figure 18-5
Regulation of transcription initiation : examples from prokaryotes
Lac operon
Catabolite activator protein (CAP: CRP-cAMP receptor)
Figure 18-5
Regulation of transcription initiation : examples from prokaryotes
Lac operon
catabolite activator protein 9

10. Figure 18-6
Expression of lac gene
Figure 18-6
Expression 10

11. Symmetric half sites of lac operator
Figure 18-7
Symmetric half sites of lac operator
Figure 18-7
Symmetric half sites 11

12. Control region of lac operon
Figure 18-8
Control region of lac operon
Figure 18-8
Control region of lac operon 12

13. Figure 18-9
Activation of lac promoter by CAP (activating region bind to C-term of RNA pol)
Figure 18-9
Activation of lac promoter by CAP 13

14. Structure of CAP-αCTD(of RNA Pol)-DNA complex
Figure 18-10
Structure of CAP-αCTD(of RNA Pol)-DNA complex
activating region
Figure 18-10
Structure of CAP-αCTD-DNA complex
DNA binding region
DNA binding region 14

15. Binding of a protein with a helix-turn-helix motif to DNA
Figure 18-11
Binding of a protein with a helix-turn-helix motif to DNA
Figure 18-11
Binding of a protein with a helix-turn-helix motif to DNA 15

16. Lac repressor binds as a tetramer to two operators
Figure 18-12
Lac repressor binds as a tetramer to two operators
Figure 18-12
Lac repressor binds as a tetramer to two operators. 16

17. Inducer of lac operon is allolactose.
Figure 18-13
Inducer of lac operon is allolactose.
Lactose is converted into allolactose that binds to repressor.
Figure 18-13
Inducer of Lac operon is allolactose.
Substrate for assay, releasing blue color
Synthetic inducer 17

18. CRP: cAMP receptor protein
Figure 18-14
Mechanism of allosteric (다른자리입체성) control(제어) of CAP(catabolite activator protein or CRP)
Figure 18-14
Mechanism of allosteric control of CAP
CRP: cAMP receptor protein
CRP: cAMP receptor protein 18

19. Figure 18-15
Alternative sigma factors (other sigma factor than 70)control the ordered expression of genes in a bacterial virus (in here B. subtilis bacteriophage SPO1)
Figure 18-15
Alternative sigma factors control the ordered expression of genes in a bacterial virus (bacteriophage)
Other alternative sigma factors in stead of sigma 70 are used under certain circumstances, i.e. heat shock sigma factor 32, etc.) 19

20. In recruitment, activators bring RNA Pol .
Figure 18-16
NtrC and MerR : Transcriptional activators that work by allostery rather than recruitment.
In recruitment, activators bring RNA Pol .
In contrast in allostery, RNA Pol bind to promoter first as inactive complex but triggered by activator (NtrC and MerR).
Allosteric transcriptional activator (NtrC)
Figure 18-16
NtrC and MerR : Transcriptional activators that work by allostery rather than recrutiment
Allosteric transcriptional activator 20

21. Figure 18-17
Allosteric transcriptional activator (MerR): activate transcription by twisting promoter DNA
twist
Figure 18-17
twist 21

22. Structure of a MerT like promoter
Figure 18-18
Structure of a MerT like promoter
Active form
Figure 18-18
Structure of a MerT like promoter
Active form 22

23. Some repressors hold RNA polymerase at the promoter rather than excluding.
i.e. E. coli Gal repressor and PA2C binding repressor P4 protein (in Ф29 phage of B. subtilis)
so strongly bind to RNA pol that polymerase is unable to escape the promoter.
Some repressors hold RNA polymerase at the promoter rather than excluding.
i.e. E. coli Gal repressor, PA2C binding repressor P4 protein so strongly bind to RNA pol that polymerase is unable to escape the promoter.

24. Figure 18-19
Control of the araBAD operon and the promoter is also controlled by CAP
Arabinose binds to AraC, changing the shape of the activator
CAP binding site is just upstream of araI1 and araI2
Figure 18-19
Control of the araBAD operon
Arabinose
CAP binding site is just upstream of araI1 and araI2 24

25. Box
Quorom sensing of LuxR
Box
Quorom sensing of LuxR 25

26. The case of bacteriophage lambda : layers of regulation

27. Growth and Induction of lambda lysogen
Figure 18-20
Growth and Induction of lambda lysogen
Figure 18-20
The case of bacteriophage lambda : layers of regulation
prophage
prophage 27

28. Map of phage λ in the circular form
Figure 18-21
Map of phage λ in the circular form
Figure 18-21
Map of phage λ in the circular form 28

29. Promoters in the right and left control regions of phage λ
Figure 18-22
Promoters in the right and left control regions of phage λ
Cro (Control of repressor and
other things)
λ repressor gene (cI)
Figure 18-22
Promoters in the right and left control regions of phage
λ repressor gene
Control of repressor and other things 29

30. Transcription in the λ control regions
Figure 18-23
Transcription in the λ control regions
Figure 18-23 30

31. Figure 18-24
λ repressor (monomer)
Figure 18-24
λ repressor 31

32. cI expression: lysogenic cro expression: lytic
Figure 18-25
cI expression: lysogenic
cro expression: lytic
Figure 18-25 32

33. Figure 18-26
λ repressor
dimer
Figure 18-26
dimer 33

34. Figure 18-27
Figure 18-27 34

35. Figure 18-28
Figure 18-28 35

36. Genes and promoters involved in the lytic and lysogenic choice
Figure 18-30
Genes and promoters involved in the lytic and lysogenic choice
cI expression: lysogenic
cro expression: lytic
Figure 18-30
Also cII and cIII (control decision of between lytic and lysogenic) expression: lysogenic
These are transcriptional activator s binding PRE and stimulate cI gene expression. 36

37. Box
Box 37

38. Establishment of lysogeny
Figure 18-31
Establishment of lysogeny
Figure 18-31
Establishment of lysogeny 38

39. In transcriptional antitermination in a lambda development
N gene regulates(express) early gene expression by acting at three terminators: to the left of N, to the right of cro, between P and Q

40. Figure 18-32
Recognition sites and sites of action of the lambda N and Q transcription antiterminators (positive transcriptional regulation)
(In transcriptional anti-termination(no termination) in a lambda development)
N binds to the left of N, to the right of cro, between P and Q
Initial terminator
N on the left of PR
Figure 18-32
Region for essential Q protein function
Initial terminator .
Terminator
Region for essential Q protein function (Q recognize QBE): late gene expression 40

41. How λ Q engage in RNA pol during early elongation
Figure 18-33
How λ Q engage in RNA pol during early elongation
Figure 18-33
How λ Q engage in RNA pol during early elongation 41

42. Figure 18-34
DNA site and transcribed RNA structures active in retroregulation of int (integrase)
Figure 18-34
DNA site and transcribed RNA structures active in retroregulation of int
Not degraded if no N protein
degraded if N protein (in lytic)
(anti-terminate at terminator) is present.
Not degraded if no N protein (lysogeny)
(terminate at terminator) 42

44. Retroregulation (degradation proceeds backwards basically through the gene but not by enzyme)
RNA initiated at PI stops at a terminator about 300 nucleotides after end of the int (integrase) gene
(this short mRNA stable)
RNA initiated at PL is transcribed beyond the terminator. This longer mRNA is degraded by nuclease (when lytic is favored and at low cII activity).

45. When prophage is induced (meaning virus escapes from bacteria), phage needs to make integrase that is transcribed by PL but this is not degraded.
During lysogeny establishment, phage attachment site is between the end of int gene and those sequences encoding the extended stem from which mRNA degradation is begun.
Thus the site causing degradation is removed from the end of int gene, and so mRNA made from PL is stable.
When prophage is induced (meaning virus escape from bacteria), phage needs to make integrase that is transcribed by PL but this is not degraded.